Following a $35 million upgrade of the Queenscliff Harbour, some berth owners have been hit with fee increases from $780 per annum, to $6,500 a year.
The Age says this compares to Apollo Bay and San Remo, where owners pay about $2,000 a year.
Queenscliff boat owners are on a five year memoratorium on fees, but will need to pay from 2011.
Harvour spokeswoman Jenni Coutts told The Age berthing fees at Queenscliff had not risen for more than ten years.
"The point is that there is a berth option that will cost approximately what berth holders are paying now," she said.